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parse amount of threads to beagle #10

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parse amount of threads to beagle #10

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4 changes: 2 additions & 2 deletions process.smake
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ rule phase_with_ref:
ref_sample = get_ref_sample()
threads: 64
shell:
"beaglew impute=false gt={input} ref={params.ref_sample}/{wildcards.file}.vcf.gz out={params.prefix}"
"beaglew impute=false gt={input} ref={params.ref_sample}/{wildcards.file}.vcf.gz out={params.prefix} nthreads={threads}"

#
# Phase WITHOUT Reference Geonme
Expand All @@ -34,7 +34,7 @@ rule phase_without_ref:
prefix="{dir}_PH/{file}"
threads: 64
shell:
"beaglew impute=false gt={input} out={params.prefix}"
"beaglew impute=false gt={input} out={params.prefix} nthreads={threads}"


#
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